Unveiling the Secrets of Microbial Dark Matter
In the vast realm of microbial life, there exists a mysterious and largely unexplored territory known as "microbial dark matter." This term refers to the countless species of bacteria and archaea that thrive on our planet, yet remain largely unknown and unstudied. However, a recent research endeavor has shed light on this enigmatic world, offering a glimmer of hope in the fight against climate change.
The Quest for CO2-Fixing Microorganisms
At the heart of this research is the RIKEN BioResource Research Center (BRC), a hub of scientific innovation located in Tsukuba, Japan. BRC's mission is to collect, manage, and distribute high-quality biological resources, ensuring the reproducibility of experiments and the credibility of scientific research. Among its vast collection are microbial strains, carefully curated and made available to researchers worldwide.
The current project, led by the Microbe Division at BRC, focused on exploring the potential of these microorganisms to capture carbon dioxide (CO2). By analyzing the genomes of approximately 6,700 microbial strains, the researchers discovered that around 300 of them possess genes involved in CO2 fixation. This finding could have significant implications for reducing CO2 emissions and mitigating global warming.
Unlocking the Secrets of Prokaryotes
The collection at BRC is vast, containing over 32,000 microbial strains, with approximately 21,000 strains made publicly available. These strains, discovered and cultured by microbiologists worldwide, provide a treasure trove of information. In addition to genomic data, BRC collects valuable experimental and culturing data, such as the environments in which the microorganisms were found and their growth conditions.
The researchers decided to delve into the CO2 fixation capabilities of these microorganisms, specifically focusing on the Calvin-Benson cycle, a series of chemical reactions responsible for CO2 fixation in plants and some microorganisms. Arisa Nishihara, a postdoctoral researcher on the team, expressed her excitement about the project, despite its challenging nature.
Exploring the Calvin-Benson Cycle
Plants, through photosynthesis, capture CO2 from the atmosphere and convert it into organic compounds. The Calvin-Benson cycle is at the core of this process. However, plants are not the only organisms capable of carbon fixation. Many microorganisms, including bacteria and archaea, can utilize this cycle or other carbon-fixation pathways, even in complete darkness.
The researchers analyzed the genomes of 6,749 JCM strains, searching for genes associated with the Calvin-Benson cycle. Simultaneously, they cross-referenced this data with existing literature to determine whether the microorganisms were indeed capable of CO2 fixation. This systematic approach filled a gap in concrete research, connecting genomic data with scientific literature.
Uncovering Promising Candidates
After a two-year analysis process, the researchers identified 306 strains carrying genes associated with the Calvin-Benson cycle. These strains belonged to 147 genera, with evidence of CO2 fixation found in 74 of those genera. Nishihara explained that some of these genera were already being utilized in research, while the remaining 73 genera represent promising candidates for further exploration.
The research team then focused on the enzyme Rubisco, which catalyzes a key step in the Calvin-Benson cycle. By classifying the 306 strains based on their type, habitat, and metabolic properties, they discovered significant differences in energy sources and habitats. Using genetic data, they identified 173 strains with potential CO2 fixation abilities, despite belonging to genera where no previous CO2 fixation had been reported.
Enhancing the Value of Microbial Collections
This meticulous research enhances the value of the microbial collection at BRC. By specifically noting "CO2 fixation" as a characteristic in the catalog, researchers worldwide can more easily select microorganisms suited to their CO2 fixation goals. Nishihara expressed her desire to continue gathering high-quality primary data on microbial habitats and culture conditions, contributing to the TRIP initiative at RIKEN.
The TRIP initiative aims to connect cutting-edge research infrastructure and data across disciplines, with a focus on organizing high-quality data, achieving breakthroughs in quantum chemical calculations, and creating predictive science. BRC's research plays a crucial role in compiling primary data, but the team aims to go further, utilizing AI to add value and make predictions about the potential applications of these microorganisms.
A Step Towards a Low-Carbon Society
The discovery of microorganisms with CO2 fixation capabilities offers a promising avenue for reducing CO2 emissions. As Shingo Kato, a senior research scientist, explained, harnessing the ability of microorganisms to fix CO2 in places where light doesn't reach could contribute to the realization of a low-carbon society.
This research highlights the importance of exploring and understanding the vast and diverse world of microorganisms. By uncovering the secrets of microbial dark matter, we may find innovative solutions to some of the most pressing challenges facing our planet.
